Build log

tree-puzzle-5.2:20091220-044809.log (text/plain), 33.97 KB, created by Diego Elio Pettenò (RETIRED) on 2009-12-20 13:55:45 UTC

 [32;01m*[0m CPV:  sci-biology/tree-puzzle-5.2
 [32;01m*[0m REPO: gentoo
 [32;01m*[0m USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking tree-puzzle-5.2.tar.gz to /var/tmp/portage/sci-biology/tree-puzzle-5.2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/tree-puzzle-5.2/work
>>> Compiling source in /var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2 ...
 * econf: updating tree-puzzle-5.2/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating tree-puzzle-5.2/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets ${MAKE}... yes
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether i686-pc-linux-gnu-gcc accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking whether i686-pc-linux-gnu-gcc and cc understand -c and -o together... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets ${MAKE}... (cached) yes
checking for mpcc... no
checking for hcc... no
checking for mpicc... /usr/bin/mpicc
checking for mpicc_lam... no
checking for mpicc_mpich... no
checking for cc... /usr/bin/cc
checking whether /usr/bin/mpicc works as MPI compiler... yes
checking whether /usr/bin/mpicc handles quotes correctly... yes
checking whether i686-pc-linux-gnu-gcc handles quotes correctly... yes
checking for main in -lm... yes
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for i686-pc-linux-gnu-gcc option to accept ANSI C... none needed
checking for an ANSI C-conforming const... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/sprng/Makefile
config.status: creating doc/Makefile
config.status: creating data/Makefile
config.status: creating tests/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
make -j14 
Making all in src
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
make  all-recursive
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
Making all in sprng
make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
i686-pc-linux-gnu-gcc        -O2 -pipe  -c makeseed.c
i686-pc-linux-gnu-gcc        -O2 -pipe  -c store.c
i686-pc-linux-gnu-gcc        -O2 -pipe  -c memory.c
i686-pc-linux-gnu-gcc        -O2 -pipe  -c checkid.c
i686-pc-linux-gnu-gcc        -O2 -pipe  -c lcg64.c 
i686-pc-linux-gnu-gcc        -O2 -pipe  -c primes-lcg64.c 
primes-lcg64.c: In function ‘getprime’:
primes-lcg64.c:75: warning: incompatible implicit declaration of built-in function ‘memcpy’
make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./gamma.c && mv gamma.o sgamma.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./ml1.c && mv ml1.o sml1.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./ml2.c && mv ml2.o sml2.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./mlparam.c && mv mlparam.o smlparam.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./model1.c && mv model1.o smodel1.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./model2.c && mv model2.o smodel2.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./puzzle1.c && mv puzzle1.o spuzzle1.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./puzzle2.c && mv puzzle2.o spuzzle2.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./pstep.c && mv pstep.o spstep.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./util.c && mv util.o sutil.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./consensus.c && mv consensus.o sconsensus.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./treesort.c && mv treesort.o streesort.o
i686-pc-linux-gnu-gcc  -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng      -O2 -pipe  -c ./treetest.c && mv treetest.o streetest.o
cd sprng && make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o 
make[4]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
make[4]: `makeseed.o' is up to date.
make[4]: `store.o' is up to date.
make[4]: `memory.o' is up to date.
make[4]: `checkid.o' is up to date.
make[4]: `lcg64.o' is up to date.
make[4]: `primes-lcg64.o' is up to date.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
./puzzle2.c: In function ‘computeallquartets’:
./puzzle2.c:1463: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
./puzzle1.c: In function ‘writeallquarts’:
./puzzle1.c:261: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
./puzzle1.c: In function ‘readallquarts’:
./puzzle1.c:294: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:295: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:297: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:298: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:299: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:322: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
./puzzle1.c:335: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
./puzzle1.c: In function ‘setoptions’:
./puzzle1.c:718: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:776: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:795: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:813: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:915: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1115: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1149: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1164: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1181: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1449: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1478: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1502: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1515: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1524: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1533: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1542: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1551: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
./puzzle1.c:1560: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result
i686-pc-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o  sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o  -lm  -o puzzle
make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
Making all in doc
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
Making all in data
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data'
Making all in tests
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2'
>>> Source compiled.
>>> Test phase [check]: sci-biology/tree-puzzle-5.2
make -j14 -j1 check 
Making check in src
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
Making check in sprng
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
cd sprng && make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o 
make[3]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
make[3]: `makeseed.o' is up to date.
make[3]: `store.o' is up to date.
make[3]: `memory.o' is up to date.
make[3]: `checkid.o' is up to date.
make[3]: `lcg64.o' is up to date.
make[3]: `primes-lcg64.o' is up to date.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src/sprng'
i686-pc-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o  sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o  -lm  -o puzzle
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/src'
Making check in doc
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/doc'
Making check in data
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/data'
Making check in tests
make[1]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'
make  check-TESTS
make[2]: Entering directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'

Testing: binary data, quartet puzzling (qp-pure-bin)
PASS: qp-pure-bin.test

Testing: nucleotide data, default model, quartet puzzling (qp-pure-nucl)
101c101
< Thylacinus  0.00000  0.25  0.22032  0.24509  0.26007  0.24938  0.22246
---
> Thylacinus  0.00000  0.25562  0.22032  0.24509  0.26007  0.24938  0.22246
103c103
< Sarcophilu  0.25  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
---
> Sarcophilu  0.25562  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
109c109
< Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28
---
> Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28562
113c113
< Philander   0.22246  0.26008  0.17801  0.23041  0.28  0.29036  0.00000
---
> Philander   0.22246  0.26008  0.17801  0.23041  0.28562  0.29036  0.00000
278c278
< Dasyurus      3  0.00  0.01273      11  0.04220  0.02513
---
> Dasyurus      3  0.00572  0.01273      11  0.04220  0.02513
290c290
< ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995,
---
> ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995,
FAIL: qp-pure-nucl.test

Testing: nucleotide data, TN, quartet puzzling (qp-tn-nucl)
24,25c24,25
< Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.40)
< Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.68)
---
> Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.61)
> Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.65)
102c102
< Thylacinus  0.00000  0.25968  0.22378  0.26  0.26619  0.25302  0.22610
---
> Thylacinus  0.00000  0.25968  0.22378  0.25026  0.26619  0.25302  0.22610
108c108
< Echymipera  0.26  0.27376  0.20328  0.00000  0.30289  0.34430  0.23479
---
> Echymipera  0.25026  0.27376  0.20328  0.00000  0.30289  0.34430  0.23479
113c113
<             0.33
---
>             0.33582
116c116
< Bos         0.24162  0.30169  0.24235  0.27773  0.27782  0.33  0.22749
---
> Bos         0.24162  0.30169  0.24235  0.27773  0.27782  0.33582  0.22749
277c277
< Thylacinus    1  0.11472  0.03957       9  0.04  0.03453
---
> Thylacinus    1  0.11472  0.03957       9  0.05924  0.03453
280c280
< Echymipera    4  0.14312  0.04216      12  0.09  0.03071
---
> Echymipera    4  0.14312  0.04216      12  0.05429  0.03071
290c290
< (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.04,
---
> (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.05924,
292c292
< Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.09);
---
> Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.05429);
FAIL: qp-tn-nucl.test

Testing: nucleotide data, HKY, clock, quartet puzzling (qp-hky-clock-nucl)
101c101
< Thylacinus  0.00000  0.25  0.22032  0.24509  0.26007  0.24938  0.22246
---
> Thylacinus  0.00000  0.25562  0.22032  0.24509  0.26007  0.24938  0.22246
103c103
< Sarcophilu  0.25  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
---
> Sarcophilu  0.25562  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
109c109
< Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28
---
> Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28562
113c113
< Philander   0.22246  0.26008  0.17801  0.23041  0.28  0.29036  0.00000
---
> Philander   0.22246  0.26008  0.17801  0.23041  0.28562  0.29036  0.00000
278c278
< Dasyurus      3  0.00  0.01273      11  0.04220  0.02513
---
> Dasyurus      3  0.00572  0.01273      11  0.04220  0.02513
290c290
< ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995,
---
> ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995,
FAIL: qp-hky-clock-nucl.test

Testing: nucleotide data, HKY, rate heterogeneity, quartet puzzling (qp-hky-rhet-nucl)
24c24
< Transition/transversion parameter (estimated from data set): 2.96 (S.E. 0.79)
---
> Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84)
29c29
<  A-G rate: 5.85999
---
>  A-G rate: 5.85063
32c32
<  C-T rate: 5.85999
---
>  C-T rate: 5.85063
42c42
< Expected transition/transversion ratio: 3.15
---
> Expected transition/transversion ratio: 3.14
101,115c101,115
< Thylacinus  0.00000  0.52969  0.37917  0.68  0.58959  0.56187  0.43958
<             0.55330
< Sarcophilu  0.52969  0.00000  0.17842  0.62570  0.69939  0.93662  0.62369
<             0.78648
< Dasyurus    0.37917  0.17842  0.00000  0.39056  0.53463  0.60411  0.31937
<             0.60
< Echymipera  0.68  0.62570  0.39056  0.00000  0.70269  0.94339  0.42036
<             0.66107
< Trichosuru  0.58959  0.69939  0.53463  0.70269  0.00000  0.39438  0.70062
<             0.62735
< Phalanger   0.56187  0.93662  0.60411  0.94339  0.39438  0.00000  0.78715
<             0.98990
< Philander   0.43958  0.62369  0.31937  0.42036  0.70062  0.78715  0.00000
<             0.49297
< Bos         0.55330  0.78648  0.60  0.66107  0.62735  0.98990  0.49297
---
> Thylacinus  0.00000  0.52940  0.37900  0.52236  0.58922  0.56150  0.43932
>             0.55291
> Sarcophilu  0.52940  0.00000  0.17837  0.62532  0.69892  0.93602  0.62327
>             0.78596
> Dasyurus    0.37900  0.17837  0.00000  0.39032  0.53431  0.60369  0.31919
>             0.56220
> Echymipera  0.52236  0.62532  0.39032  0.00000  0.70229  0.94283  0.42016
>             0.66063
> Trichosuru  0.58922  0.69892  0.53431  0.70229  0.00000  0.39416  0.70017
>             0.62697
> Phalanger   0.56150  0.93602  0.60369  0.94283  0.39416  0.00000  0.78658
>             0.98921
> Philander   0.43932  0.62327  0.31919  0.42016  0.70017  0.78658  0.00000
>             0.49264
> Bos         0.55291  0.78596  0.56220  0.66063  0.62697  0.98921  0.49264
118,120c118,120
< Average distance (over all possible pairs of sequences):  0.59133
<                   minimum  : 0.17842,  maximum  : 0.98990
<                   variance : 0.03587,  std.dev. : 0.18939
---
> Average distance (over all possible pairs of sequences):  0.59096
>                   minimum  : 0.17837,  maximum  : 0.98921
>                   variance : 0.03581,  std.dev. : 0.18924
300,307c300,307
< Thylacinus    1  0.23379  0.10258       9  0.19946  0.09586
< Sarcophilu    2  0.18915  0.06717      10  0.22314  0.13107
< Dasyurus      3  0.00001  0.00689
< Echymipera    4  0.27862  0.11701
< Trichosuru    5  0.17838  0.10170
< Phalanger     6  0.27546  0.12626
< Philander     7  0.22555  0.10280     10 iterations until convergence
< Bos           8  0.38549  0.14583     log L: -570.33
---
> Thylacinus    1  0.23363  0.10248       9  0.19927  0.09576
> Sarcophilu    2  0.18905  0.06712      10  0.22291  0.13093
> Dasyurus      3  0.00001  0.00200
> Echymipera    4  0.27841  0.11691
> Trichosuru    5  0.17822  0.10160
> Phalanger     6  0.27519  0.12613
> Philander     7  0.22533  0.10269     10 iterations until convergence
> Bos           8  0.38507  0.14566     log L: -570.33
315,317c315,317
< (Thylacinus:0.23379,(Sarcophilu:0.18915,Dasyurus:0.00001)90:0.19946,
< (Trichosuru:0.17838,Phalanger:0.27546)87:0.22314,Echymipera:0.27862,
< Philander:0.22555,Bos:0.38549);
---
> (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927,
> (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841,
> Philander:0.22533,Bos:0.38507);
FAIL: qp-hky-rhet-nucl.test

Testing: nucleotide data, HKY, clock, rate heterogeneity, quartet puzzling (qp-hky-rhet-clock-nucl)
24c24
< Transition/transversion parameter (estimated from data set): 2.96 (S.E. 0.79)
---
> Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84)
29c29
<  A-G rate: 5.85999
---
>  A-G rate: 5.85063
32c32
<  C-T rate: 5.85999
---
>  C-T rate: 5.85063
42c42
< Expected transition/transversion ratio: 3.15
---
> Expected transition/transversion ratio: 3.14
101,115c101,115
< Thylacinus  0.00000  0.52969  0.37917  0.68  0.58959  0.56187  0.43958
<             0.55330
< Sarcophilu  0.52969  0.00000  0.17842  0.62570  0.69939  0.93662  0.62369
<             0.78648
< Dasyurus    0.37917  0.17842  0.00000  0.39056  0.53463  0.60411  0.31937
<             0.60
< Echymipera  0.68  0.62570  0.39056  0.00000  0.70269  0.94339  0.42036
<             0.66107
< Trichosuru  0.58959  0.69939  0.53463  0.70269  0.00000  0.39438  0.70062
<             0.62735
< Phalanger   0.56187  0.93662  0.60411  0.94339  0.39438  0.00000  0.78715
<             0.98990
< Philander   0.43958  0.62369  0.31937  0.42036  0.70062  0.78715  0.00000
<             0.49297
< Bos         0.55330  0.78648  0.60  0.66107  0.62735  0.98990  0.49297
---
> Thylacinus  0.00000  0.52940  0.37900  0.52236  0.58922  0.56150  0.43932
>             0.55291
> Sarcophilu  0.52940  0.00000  0.17837  0.62532  0.69892  0.93602  0.62327
>             0.78596
> Dasyurus    0.37900  0.17837  0.00000  0.39032  0.53431  0.60369  0.31919
>             0.56220
> Echymipera  0.52236  0.62532  0.39032  0.00000  0.70229  0.94283  0.42016
>             0.66063
> Trichosuru  0.58922  0.69892  0.53431  0.70229  0.00000  0.39416  0.70017
>             0.62697
> Phalanger   0.56150  0.93602  0.60369  0.94283  0.39416  0.00000  0.78658
>             0.98921
> Philander   0.43932  0.62327  0.31919  0.42016  0.70017  0.78658  0.00000
>             0.49264
> Bos         0.55291  0.78596  0.56220  0.66063  0.62697  0.98921  0.49264
118,120c118,120
< Average distance (over all possible pairs of sequences):  0.59133
<                   minimum  : 0.17842,  maximum  : 0.98990
<                   variance : 0.03587,  std.dev. : 0.18939
---
> Average distance (over all possible pairs of sequences):  0.59096
>                   minimum  : 0.17837,  maximum  : 0.98921
>                   variance : 0.03581,  std.dev. : 0.18924
300,307c300,307
< Thylacinus    1  0.23379  0.10258       9  0.19946  0.09586
< Sarcophilu    2  0.18915  0.06717      10  0.22314  0.13107
< Dasyurus      3  0.00001  0.00689
< Echymipera    4  0.27862  0.11701
< Trichosuru    5  0.17838  0.10170
< Phalanger     6  0.27546  0.12626
< Philander     7  0.22555  0.10280     10 iterations until convergence
< Bos           8  0.38549  0.14583     log L: -570.33
---
> Thylacinus    1  0.23363  0.10248       9  0.19927  0.09576
> Sarcophilu    2  0.18905  0.06712      10  0.22291  0.13093
> Dasyurus      3  0.00001  0.00200
> Echymipera    4  0.27841  0.11691
> Trichosuru    5  0.17822  0.10160
> Phalanger     6  0.27519  0.12613
> Philander     7  0.22533  0.10269     10 iterations until convergence
> Bos           8  0.38507  0.14566     log L: -570.33
315,317c315,317
< (Thylacinus:0.23379,(Sarcophilu:0.18915,Dasyurus:0.00001)90:0.19946,
< (Trichosuru:0.17838,Phalanger:0.27546)87:0.22314,Echymipera:0.27862,
< Philander:0.22555,Bos:0.38549);
---
> (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927,
> (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841,
> Philander:0.22533,Bos:0.38507);
351,358c351,358
< Thylacinus    1  0.29802    0.784       9  0.20377    0.979
< Sarcophilu    2  0.09425    2.007      10  0.22869    0.976
< Dasyurus      3  0.09425    0.000
< Echymipera    4  0.29802    0.935
< Trichosuru    5  0.23493    0.759
< Phalanger     6  0.23493    1.173
< Philander     7  0.29802    0.757     16 iterations until convergence
< Bos           8  0.29802    1.294     log L: -573.89
---
> Thylacinus    1  0.29776    0.785       9  0.20356    0.979
> Sarcophilu    2  0.09420    2.007      10  0.22846    0.976
> Dasyurus      3  0.09420    0.000
> Echymipera    4  0.29776    0.935
> Trichosuru    5  0.23472    0.759
> Phalanger     6  0.23472    1.172
> Philander     7  0.29776    0.757     16 iterations until convergence
> Bos           8  0.29776    1.293     log L: -573.89
361,364c361,364
< 0.23493  0.07639    10  5  6  
< 0.09425  0.03155    9  2  3  
< 0.29802  0.05406    10  4  7  8  1  9  
< 0.38082  0.07038   of root at branch 10
---
> 0.23472  0.07631    10  5  6  
> 0.09420  0.03153    9  2  3  
> 0.29776  0.05401    10  4  7  8  1  9  
> 0.38047  0.07031   of root at branch 10
370,372c370,372
< ((Trichosuru:0.23493,Phalanger:0.23493)87:0.14589,(Echymipera:0.29802,
< Philander:0.29802,Bos:0.29802,Thylacinus:0.29802,(Sarcophilu:0.09425,
< Dasyurus:0.09425)90:0.20377):0.08280);
---
> ((Trichosuru:0.23472,Phalanger:0.23472)87:0.14575,(Echymipera:0.29776,
> Philander:0.29776,Bos:0.29776,Thylacinus:0.29776,(Sarcophilu:0.09420,
> Dasyurus:0.09420)90:0.20356):0.08271);
FAIL: qp-hky-rhet-clock-nucl.test

Testing: protein data, default model, quartet puzzling (qp-pure-prot)
247,248c247,248
< HBA_HUMAN     3  0.02555  0.02185      10  0.34694  0.12
< HBA_HORSE     4  0.09  0.03153      11  0.60239  0.11261
---
> HBA_HUMAN     3  0.02555  0.02185      10  0.34694  0.12552
> HBA_HORSE     4  0.09542  0.03153      11  0.60239  0.11261
257c257
< (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09)100:0.28345,
---
> (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345,
FAIL: qp-pure-prot.test

Testing: protein data, mtREV, quartet puzzling (qp-mtrev-prot)
107c107
< HBA_HORSE   1.16856  1.20524  0.13144  0.00000  2.44163  1.55  3.05140
---
> HBA_HORSE   1.16856  1.20524  0.13144  0.00000  2.44163  1.55582  3.05140
109c109
< GLB5_PETMA  2.15305  2.18071  1.43785  1.55  2.62256  0.00000  2.97722
---
> GLB5_PETMA  2.15305  2.18071  1.43785  1.55582  2.62256  0.00000  2.97722
FAIL: qp-mtrev-prot.test

Testing: protein data, VT, quartet puzzling (qp-vt-prot)
244c244
< HBB_HUMAN     1  0.04599  0.03062       8  0.42025  0.11482
---
> HBB_HUMAN     1  0.04599  0.03062       8  0.42025  0.11481
246c246
< HBA_HUMAN     3  0.03150  0.02213      10  0.96  0.10035
---
> HBA_HUMAN     3  0.03150  0.02213      10  0.54296  0.10035
257c257
< 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.96,
---
> 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.54296,
FAIL: qp-vt-prot.test

Testing: protein data, WAG, quartet puzzling (qp-wag-prot)
244c244
< HBB_HUMAN     1  0.08  0.03102       8  0.44299  0.11946
---
> HBB_HUMAN     1  0.05028  0.03102       8  0.44299  0.11946
246c246
< HBA_HUMAN     3  0.02934  0.02190      10  0.57110  0.10504
---
> HBA_HUMAN     3  0.02934  0.02189      10  0.57110  0.10504
256c256
< (HBB_HUMAN:0.08,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501)
---
> (HBB_HUMAN:0.05028,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501)
FAIL: qp-wag-prot.test

Testing: default data, default model, clock, quartet puzzling (qp-clock)
101c101
< Thylacinus  0.00000  0.25  0.22032  0.24509  0.26007  0.24938  0.22246
---
> Thylacinus  0.00000  0.25562  0.22032  0.24509  0.26007  0.24938  0.22246
103c103
< Sarcophilu  0.25  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
---
> Sarcophilu  0.25562  0.00000  0.13169  0.26969  0.28414  0.32680  0.26008
109c109
< Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28
---
> Trichosuru  0.26007  0.28414  0.24821  0.29531  0.00000  0.21136  0.28562
113c113
< Philander   0.22246  0.26008  0.17801  0.23041  0.28  0.29036  0.00000
---
> Philander   0.22246  0.26008  0.17801  0.23041  0.28562  0.29036  0.00000
278c278
< Dasyurus      3  0.00  0.01273      11  0.04220  0.02513
---
> Dasyurus      3  0.00572  0.01273      11  0.04220  0.02513
290c290
< ((Sarcophilu:0.13180,Dasyurus:0.00)98:0.08585,(Philander:0.08995,
---
> ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995,
FAIL: qp-clock.test

Testing: protein data, JTT, quartet puzzling (qp-jtt-prot)
106,107c106,107
< HBA_HUMAN   0.93732  0.97297  0.00000  0.12200  1.93956  1.26  2.51688
< HBA_HORSE   0.96340  0.97742  0.12200  0.00000  1.99570  1.34817  2.47
---
> HBA_HUMAN   0.93732  0.97297  0.00000  0.12200  1.93956  1.25126  2.51688
> HBA_HORSE   0.96340  0.97742  0.12200  0.00000  1.99570  1.34817  2.47562
109,110c109,110
< GLB5_PETMA  1.74159  1.75271  1.26  1.34817  2.04426  0.00000  2.23399
< LGB2_LUPLU  2.60857  2.65715  2.51688  2.47  2.69086  2.23399  0.00000
---
> GLB5_PETMA  1.74159  1.75271  1.25126  1.34817  2.04426  0.00000  2.23399
> LGB2_LUPLU  2.60857  2.65715  2.51688  2.47562  2.69086  2.23399  0.00000
245c245
< HBB_HORSE     2  0.12734  0.03889       9  0.25371  0.08
---
> HBB_HORSE     2  0.12734  0.03889       9  0.25371  0.08572
FAIL: qp-jtt-prot.test

Testing: protein data, JTT, rate heterogeneity, quartet puzzling (qp-jtt-rhet-prot)
270c270
< HBB_HUMAN     1  0.04933  0.03409       8  0.50700  0.17282
---
> HBB_HUMAN     1  0.04933  0.03409       8  0.50700  0.17281
FAIL: qp-jtt-rhet-prot.test

Testing: protein data, JTT, clock, rate heterogeneity, quartet puzzling (qp-jtt-rhet-clock-prot)
270c270
< HBB_HUMAN     1  0.04933  0.03409       8  0.50700  0.17282
---
> HBB_HUMAN     1  0.04933  0.03409       8  0.50700  0.17281
316c316
< HBB_HUMAN     1  0.08775    0.       8  0.58020    0.874
---
> HBB_HUMAN     1  0.08775    0.562       8  0.58020    0.874
FAIL: qp-jtt-rhet-clock-prot.test

Testing: protein data, default model, likelihood mapping (lm-pure-prot)
PASS: lm-pure-prot.test

Testing: protein data, default model, user tree evaluation (ut-pure-prot)
151c151
< HBB_HORSE     2  0.12686  0.03876       9  0.00001  0.00265
---
> HBB_HORSE     2  0.12686  0.03876       9  0.00001  0.00141
192,193c192,193
< HBB_HORSE     2  0.12604  0.03871       9  0.18149  0.13086
< HBA_HUMAN     3  0.02555  0.02185      10  0.34695  0.12
---
> HBB_HORSE     2  0.12604  0.03871       9  0.18149  0.13088
> HBA_HUMAN     3  0.02555  0.02185      10  0.34695  0.12552
196c196
< GLB5_PETMA    6  0.57473  0.13844     9 iterations until convergence
---
> GLB5_PETMA    6  0.57473  0.13845     9 iterations until convergence
271c271
< HBA_HUMAN     3  0.02653  0.02208      10  0.60481  0.11282
---
> HBA_HUMAN     3  0.02653  0.02208      10  0.60481  0.11281
FAIL: ut-pure-prot.test

Testing: protein data, default model, consensus construction (cons-pure-prot)
PASS: cons-pure-prot.test

***
***  !!! Important remark !!!
***
***  Please note that only the output file *.puzzle is checked
***  for identity. The overall precision reached in the program
***  is heavily dependent on the compiler as well as the optimization
***  level (-O) used to compile the executable.
***  Hence, even if tests are marked as failed this might just be
***  due to differences in less significant digits caused by rounding
***  errors from less acurate computations for the sake of faster
***  running times. (If you want to be sure about this please refer
***  to your compiler's manual!)
***
***  Please check the output file differences which are printed during the tests.
***  The template files which the results are checked against have been
***  generated with TREE-PUZZLE 5.2 compiled with GCC version 3.3-20030226
***  and default compiler flags '-g -O2' and using the SPRNG random number
***  generator.
***

=====================
14 of 17 tests failed
=====================
make[2]: *** [check-TESTS] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2/tests'
make: *** [check-recursive] Error 1
 [31;01m*[0m ERROR: sci-biology/tree-puzzle-5.2 failed:
 [31;01m*[0m   Make check failed. See above for details.
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line   61:  Called src_test
 [31;01m*[0m   environment, line 1069:  Called _eapi0_src_test
 [31;01m*[0m     ebuild.sh, line  626:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   			hasq test $FEATURES && die "Make check failed. See above for details."
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/tree-puzzle-5.2',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/tree-puzzle-5.2'.
 [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-biology/tree-puzzle-5.2:20091220-044809.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/tree-puzzle-5.2/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/tree-puzzle-5.2/work/tree-puzzle-5.2'

>>> Install tree-puzzle-5.2 into /var/tmp/portage/sci-biology/tree-puzzle-5.2/image/ category sci-biology
>>> Completed installing tree-puzzle-5.2 into /var/tmp/portage/sci-biology/tree-puzzle-5.2/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/puzzle

 [33;01m*[0m QA Notice: Package has poor programming practices which may compile
 [33;01m*[0m            fine but exhibit random runtime failures.
 [33;01m*[0m primes-lcg64.c:75: warning: incompatible implicit declaration of built-in function ‘memcpy’

 [33;01m*[0m Please do not file a Gentoo bug and instead report the above QA
 [33;01m*[0m issues directly to the upstream developers of this software.
 [33;01m*[0m Homepage: http://www.tree-puzzle.de
 [32;01m*[0m Removing /usr/share/doc
 [32;01m*[0m Removing /usr/share/info